It's a combination of things. When you're pigeon toed, the ankles can't flex properly, especially under load. Set your cleats to a neutral position and concentrate on having a near level foot and keeping the heels in at the bottom of the stroke. If you can't do this when you're going hard, don't go hard until you can. Your're training the feet for more natural mechanics. Training means stepping back and relearning sometimes. Also check the setback of the cleats. Moving the cleats so the ball of the foot is at least a couple mm ahead of the pedal axle stabilizes the heel and ankle.